chr8-144360047-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001363118.2(SLC52A2):c.555C>T(p.Leu185=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00305 in 1,612,926 control chromosomes in the GnomAD database, including 129 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. L185L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001363118.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC52A2 | NM_001363118.2 | c.555C>T | p.Leu185= | synonymous_variant | 3/5 | ENST00000643944.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC52A2 | ENST00000643944.2 | c.555C>T | p.Leu185= | synonymous_variant | 3/5 | NM_001363118.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00373 AC: 568AN: 152188Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00853 AC: 2133AN: 250092Hom.: 44 AF XY: 0.00734 AC XY: 994AN XY: 135514
GnomAD4 exome AF: 0.00297 AC: 4343AN: 1460620Hom.: 121 Cov.: 31 AF XY: 0.00288 AC XY: 2090AN XY: 726610
GnomAD4 genome ? AF: 0.00374 AC: 570AN: 152306Hom.: 8 Cov.: 33 AF XY: 0.00408 AC XY: 304AN XY: 74468
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 23, 2017 | p.Leu185Leu in exon 3 of SLC52A2: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wit hin the splice consensus sequence, and has been identified in 7.45% (640/8590) o f East Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac. broadinstitute.org; dbSNP rs74370046). - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 27, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Brown-Vialetto-van Laere syndrome 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
not provided Benign:1
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Dec 28, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at